Question: how to find motif across few protein sequences ?
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gravatar for Learner
4.0 years ago by
Learner 220
Learner 220 wrote:

I have a set of proteins IDs which are coming from the same organism (it does not actually matter) lets assume in both cases . either they are from the same organism or they are different. But the important thing is that they are all unregulated for cancer.

A small set of them are shown below

Q9NRK6 P61221 Q9NUJ1 P00519 Q9UKU7 Q9H845 P28330 P11310 P16219 P49748 P45954 Q9NRP4 Q9NPJ3 Q99798 P49753 Q9Y305 O14561

I want to know how to find a motif across all these IDs? (there are many websites to find motifs) but I am not sure which steps to take to get a common (if there is any) for all these bad boys

Thanks

ADD COMMENTlink modified 4.0 years ago by ALchEmiXt1.9k • written 4.0 years ago by Learner 220

You can try Meme package (http://meme-suite.org/ )

ADD REPLYlink written 4.0 years ago by Mike1.6k

Have you explored InterPro among the many websites you referred to in the OP? You may be able to find the common motifs among those IDs or amino acid sequences from there.

ADD REPLYlink written 4.0 years ago by Denise - Open Targets5.1k
0
gravatar for ALchEmiXt
4.0 years ago by
ALchEmiXt1.9k
The Netherlands
ALchEmiXt1.9k wrote:

If you have enough sequences you could try to build a profile HMM and discover signatures specific for this phenotypic group... they did so for example for Anti Microbial Resistance related genes (RESFAM).

ADD COMMENTlink written 4.0 years ago by ALchEmiXt1.9k
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